LAMMPS (10 Feb 2021)
  using 1 OpenMP thread(s) per MPI task
# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
# with various Rso setting as well as run of reference system for time comparison (real units)
# The first run writes restart file that is used by all subsequent runs.

# Run relres with Rso=6.25

units           real
atom_style      molecular
boundary        p p p
dielectric      1
special_bonds   lj/coul 0.0 0.0 0.5
bond_style      harmonic
angle_style     harmonic
dihedral_style  fourier

pair_style      lj/relres 5.75 6.25 12.0 14.0
read_data       Data.22DMH.in.real
Reading data file ...
  orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  8000 atoms
  reading velocities ...
  8000 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  3 = max dihedrals/atom
  reading bonds ...
  7000 bonds
  reading angles ...
  9000 angles
  reading dihedrals ...
  5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     5 = max # of 1-4 neighbors
     7 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.035 seconds

pair_coeff      6    6  0.175  3.905  0.0     0.0
pair_coeff      4    4  0.118  3.905  0.0     0.0
pair_coeff      2    2  0.118  3.905  1.2218  3.905
pair_coeff      5    5  0.145  3.960  0.0     0.0
pair_coeff      3    3  0.118  3.905  0.0     0.0
pair_coeff      1    1  0.05   3.8    2.9128  3.9309
pair_modify     shift yes
neighbor        2.0 bin
neigh_modify    every 2 delay 4 check yes

timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02

run 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003

@Article{Chaimovich1,
 author = {A. Chaimovich, C. Peter, K. Kremer},
 title = {Relative resolution: A hybrid formalism for fluid mixtures},
 journal = {J.~Chem.~Phys.},
 year =    2015,
 volume =  143,
 pages =   {243107}
@Article{Chaimovich2,
 author = {M. Chaimovich, A. Chaimovich},
 title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},
 journal = {J.~Chem.~Theory~Comput.},
 year =    2021,
 volume =  17,
 pages =   {1045--1059}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Neighbor list info ...
  update every 2 steps, delay 4 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/relres, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.953 | 9.953 | 9.953 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 
       0    286.85653   -328.51562    3703.8924    6839.6636    10543.556   -4875.3137    8579.2062     268531.8 
     100      293.231    -55.62132    3520.4874    6991.6533    10512.141   -4797.2633    8317.7507     268531.8 
     200    292.73476    332.40528    3456.3029    6979.8212    10436.124   -4914.7261    8371.0291     268531.8 
     300    292.56511    221.98408    3380.7472    6975.7762    10356.523   -4936.5552    8317.3024     268531.8 
     400    288.42948    117.72433     3428.113    6877.1681    10305.281   -4887.6852    8315.7982     268531.8 
     500    289.20503   -238.73381     3373.758    6895.6601    10269.418   -4947.3214    8321.0795     268531.8 
     600    292.02137    74.370782    3263.4324    6962.8115    10226.244   -4948.3906     8211.823     268531.8 
     700    290.20603    475.24398    3260.0754    6919.5273    10179.603   -4931.4093    8191.4846     268531.8 
     800    293.12504    175.54324    3156.6048    6989.1268    10145.732   -5006.7161    8163.3209     268531.8 
     900    287.78433    63.785361    3251.5393    6861.7855    10113.325    -5029.094    8280.6333     268531.8 
    1000    290.11974   -101.34839    3183.4817      6917.47    10100.952   -5002.9413     8186.423     268531.8 
Loop time of 2.12445 on 4 procs for 1000 steps with 8000 atoms

Performance: 40.669 ns/day, 0.590 hours/ns, 470.709 timesteps/s
91.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2517     | 1.3228     | 1.4636     |   7.2 | 62.27
Bond    | 0.18406    | 0.19356    | 0.20925    |   2.1 |  9.11
Neigh   | 0.12468    | 0.125      | 0.12534    |   0.1 |  5.88
Comm    | 0.25384    | 0.40233    | 0.4919     |  14.1 | 18.94
Output  | 0.00034203 | 0.00061893 | 0.00088527 |   0.0 |  0.03
Modify  | 0.052326   | 0.059507   | 0.066224   |   2.6 |  2.80
Other   |            | 0.02066    |            |       |  0.97

Nlocal:        2000.00 ave        2031 max        1964 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost:        9898.50 ave        9926 max        9869 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs:        92980.0 ave       94819 max       90517 min
Histogram: 1 0 0 1 0 0 0 0 0 2

Total # of neighbors = 371920
Ave neighs/atom = 46.490000
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0

write_restart	restart.relres.real
System init for write_restart ...

# Run relres with Rso=7.25

clear
  using 1 OpenMP thread(s) per MPI task
read_restart	restart.relres.real
Reading restart file ...
  restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
  restoring atom style molecular from restart
  orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
  2 by 1 by 2 MPI processor grid
  restoring pair style lj/relres from restart
  restoring bond style harmonic from restart
  restoring angle style harmonic from restart
  restoring dihedral style fourier from restart
  8000 atoms
  7000 bonds
  9000 angles
  5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     5 = max # of 1-4 neighbors
     7 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_restart CPU = 0.005 seconds

pair_style      lj/relres 6.75 7.25 12.0 14.0

pair_coeff      6    6  0.175  3.905  0.0     0.0
pair_coeff      4    4  0.118  3.905  0.0     0.0
pair_coeff      2    2  0.118  3.905  1.2218  3.905
pair_coeff      5    5  0.145  3.960  0.0     0.0
pair_coeff      3    3  0.118  3.905  0.0     0.0
pair_coeff      1    1  0.05   3.8    2.9128  3.9309
pair_modify     shift yes
neighbor        2.0 bin
neigh_modify    every 2 delay 4 check yes

timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
  fix style: nvt, fix ID: 2

run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
  update every 2 steps, delay 4 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/relres, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.34 | 10.34 | 10.34 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 
    1000    290.11974     21.86402    3334.7257      6917.47    10252.196   -4851.6973     8186.423     268531.8 
    1100    289.71937    460.00291    3365.0978    6907.9236    10273.021   -4881.5513    8246.6491     268531.8 
    1200     293.0828    194.76483    3348.6267    6988.1197    10336.746   -4743.4894    8092.1162     268531.8 
    1300    291.27785    153.93026    3496.2858    6945.0834    10441.369   -4753.3325    8249.6183     268531.8 
    1400    292.69435   -51.690836    3516.6743    6978.8575    10495.532   -4774.0701    8290.7445     268531.8 
    1500     290.0279    149.43706    3578.8283    6915.2801    10494.108   -4815.5857     8394.414     268531.8 
    1600    292.89473   -109.05125    3487.6652    6983.6354    10471.301   -4839.1407    8326.8059     268531.8 
    1700    290.99802   -146.06465      3496.48    6938.4111    10434.891   -4868.0031    8364.4831     268531.8 
    1800    286.48455   -45.580207    3550.2611    6830.7943    10381.055   -4766.3336    8316.5947     268531.8 
    1900     287.0735   -157.60878    3488.4248    6844.8368    10333.262   -4853.6992     8342.124     268531.8 
    2000    287.38046   -429.32757    3435.8336    6852.1558    10287.989   -4878.4345    8314.2681     268531.8 
Loop time of 2.6513 on 4 procs for 1000 steps with 8000 atoms

Performance: 32.588 ns/day, 0.736 hours/ns, 377.174 timesteps/s
89.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.5783     | 1.6371     | 1.7079     |   3.7 | 61.75
Bond    | 0.18196    | 0.19132    | 0.20276    |   1.7 |  7.22
Neigh   | 0.14093    | 0.14128    | 0.14156    |   0.1 |  5.33
Comm    | 0.50333    | 0.5809     | 0.64199    |   6.6 | 21.91
Output  | 0.00023452 | 0.00040924 | 0.00063279 |   0.0 |  0.02
Modify  | 0.066524   | 0.076747   | 0.084331   |   2.5 |  2.89
Other   |            | 0.02354    |            |       |  0.89

Nlocal:        2000.00 ave        2009 max        1981 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost:        9892.50 ave        9923 max        9868 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs:        118889.0 ave      120387 max      117552 min
Histogram: 1 0 0 1 0 1 0 0 0 1

Total # of neighbors = 475557
Ave neighs/atom = 59.444625
Ave special neighs/atom = 5.2500000
Neighbor list builds = 14
Dangerous builds = 0

# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group

clear
  using 1 OpenMP thread(s) per MPI task
read_restart	restart.relres.real
Reading restart file ...
  restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
  restoring atom style molecular from restart
  orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
  2 by 1 by 2 MPI processor grid
  restoring pair style lj/relres from restart
  restoring bond style harmonic from restart
  restoring angle style harmonic from restart
  restoring dihedral style fourier from restart
  8000 atoms
  7000 bonds
  9000 angles
  5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     5 = max # of 1-4 neighbors
     7 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_restart CPU = 0.004 seconds

pair_style      lj/relres 6.75 7.25 12.0 14.0

pair_coeff      6    6  0.175  3.905  0.0     0.0    5.75 6.25 12.0 14.0
pair_coeff      4    4  0.118  3.905  0.0     0.0    5.75 6.25 12.0 14.0
pair_coeff      2    2  0.118  3.905  1.2218  3.905  5.75 6.25 12.0 14.0
pair_coeff      5    5  0.145  3.960  0.0     0.0
pair_coeff      3    3  0.118  3.905  0.0     0.0
pair_coeff      1    1  0.05   3.8    2.9128  3.9309
pair_modify     shift yes
neighbor        2.0 bin
neigh_modify    every 2 delay 4 check yes

timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
  fix style: nvt, fix ID: 2

run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
  update every 2 steps, delay 4 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/relres, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.34 | 10.34 | 10.34 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 
    1000    290.11974    54.754001    3314.0966      6917.47    10231.567   -4872.3264     8186.423     268531.8 
    1100    289.78217    480.37221    3342.8765    6909.4211    10252.298   -4900.7266    8243.6032     268531.8 
    1200    293.25523    188.46596    3322.6257    6992.2308    10314.857   -4771.3485    8093.9742     268531.8 
    1300    291.59734    146.50303    3465.2113     6952.701    10417.912   -4782.9861    8248.1974     268531.8 
    1400    292.71873   -40.372074     3491.747    6979.4389    10471.186   -4790.7124    8282.4594     268531.8 
    1500    290.60378    120.25863    3539.5538    6929.0112    10468.565   -4849.9813    8389.5351     268531.8 
    1600    293.21218   -143.75501    3452.9516    6991.2046    10444.156   -4885.0192    8337.9708     268531.8 
    1700    291.02865   -207.34728    3465.4131    6939.1416    10404.555    -4887.363    8352.7761     268531.8 
    1800    286.00091   -91.017961    3530.3422    6819.2625    10349.605   -4807.6624    8338.0046     268531.8 
    1900     286.3006     -145.399    3485.1695    6826.4082    10311.578    -4848.263    8333.4325     268531.8 
    2000    288.43931   -469.99712    3409.0906    6877.4025    10286.493   -4905.9002    8314.9907     268531.8 
Loop time of 2.32221 on 4 procs for 1000 steps with 8000 atoms

Performance: 37.206 ns/day, 0.645 hours/ns, 430.624 timesteps/s
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.4451     | 1.5022     | 1.555      |   3.7 | 64.69
Bond    | 0.18307    | 0.19206    | 0.20526    |   2.0 |  8.27
Neigh   | 0.12827    | 0.12956    | 0.13074    |   0.3 |  5.58
Comm    | 0.36752    | 0.42006    | 0.48825    |   8.1 | 18.09
Output  | 0.00022658 | 0.00025297 | 0.0003292  |   0.0 |  0.01
Modify  | 0.05223    | 0.057658   | 0.063373   |   2.1 |  2.48
Other   |            | 0.02044    |            |       |  0.88

Nlocal:        2000.00 ave        2016 max        1981 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost:        9878.25 ave        9891 max        9868 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs:        108567.0 ave      110532 max      107467 min
Histogram: 1 1 1 0 0 0 0 0 0 1

Total # of neighbors = 434269
Ave neighs/atom = 54.283625
Ave special neighs/atom = 5.2500000
Neighbor list builds = 14
Dangerous builds = 0

# Run reference system with lj/smooth

clear
  using 1 OpenMP thread(s) per MPI task
read_restart	restart.relres.real
Reading restart file ...
  restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021
  restoring atom style molecular from restart
  orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837)
  2 by 1 by 2 MPI processor grid
  restoring pair style lj/relres from restart
  restoring bond style harmonic from restart
  restoring angle style harmonic from restart
  restoring dihedral style fourier from restart
  8000 atoms
  7000 bonds
  9000 angles
  5000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     5 = max # of 1-4 neighbors
     7 = max # of special neighbors
  special bonds CPU = 0.004 seconds
  read_restart CPU = 0.007 seconds

pair_style      lj/smooth 12.0 14.0

pair_coeff      6    6  0.175  3.905
pair_coeff      4    4  0.118  3.905
pair_coeff      2    2  0.118  3.905
pair_coeff      5    5  0.145  3.960
pair_coeff      3    3  0.118  3.905
pair_coeff      1    1  0.05   3.8
pair_modify     shift yes
neighbor        2.0 bin
neigh_modify    every 2 delay 4 check yes

timestep 1.0
thermo 100
thermo_style custom step temp press pe ke etotal epair emol vol
fix 2 all nvt temp 290 290 2.0e+02
Resetting global fix info from restart file:
  fix style: nvt, fix ID: 2

run 1000
All restart file global fix info was re-assigned
Neighbor list info ...
  update every 2 steps, delay 4 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/smooth, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.86 | 11.86 | 11.86 Mbytes
Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 
    1000    290.11974   -80.648214    3258.0256      6917.47    10175.496   -4928.3973     8186.423     268531.8 
    1100    289.70919    358.20314     3288.412    6907.6811    10196.093   -4959.5166    8247.9285     268531.8 
    1200    292.84488    96.692992    3277.1296    6982.4468    10259.576   -4818.7374     8095.867     268531.8 
    1300    291.07262    65.629153    3425.4662    6940.1899    10365.656   -4828.0862    8253.5524     268531.8 
    1400    292.39722   -113.07286    3448.8088     6971.773    10420.582   -4841.3586    8290.1674     268531.8 
    1500    289.80998    90.176596    3510.6526    6910.0843    10420.737   -4884.6145    8395.2671     268531.8 
    1600    292.48452   -180.26543    3426.6967    6973.8544    10400.551     -4903.46    8330.1567     268531.8 
    1700    291.32152   -220.54923     3421.802    6946.1246    10367.927    -4946.101    8367.9031     268531.8 
    1800    286.77292   -101.26406    3475.3166    6837.6701    10312.987    -4830.565    8305.8816     268531.8 
    1900     286.6849   -161.65289    3428.0457    6835.5713    10263.617   -4909.5924    8337.6381     268531.8 
    2000     287.3785   -477.01298    3367.9719    6852.1091    10220.081   -4962.7001    8330.6719     268531.8 
Loop time of 7.44371 on 4 procs for 1000 steps with 8000 atoms

Performance: 11.607 ns/day, 2.068 hours/ns, 134.342 timesteps/s
92.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.0092     | 6.1923     | 6.5395     |   8.2 | 83.19
Bond    | 0.18292    | 0.18861    | 0.19918    |   1.5 |  2.53
Neigh   | 0.16826    | 0.16868    | 0.1691     |   0.1 |  2.27
Comm    | 0.47602    | 0.82734    | 1.0097     |  22.7 | 11.11
Output  | 0.00023062 | 0.00025561 | 0.00032727 |   0.0 |  0.00
Modify  | 0.040804   | 0.047642   | 0.054462   |   3.1 |  0.64
Other   |            | 0.01893    |            |       |  0.25

Nlocal:        2000.00 ave        2015 max        1972 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost:        9870.50 ave        9899 max        9855 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs:        506501.0 ave      514030 max      499023 min
Histogram: 1 0 0 0 1 1 0 0 0 1

Total # of neighbors = 2026005
Ave neighs/atom = 253.25063
Ave special neighs/atom = 5.2500000
Neighbor list builds = 13
Dangerous builds = 0

Total wall time: 0:00:14
